Judd is recognised as a great at two clubs: West Coast and Carlton. During his 134 games with West Coast he captained the club for two seasons and won two Club Champion Awards. After returning to Melbourne to captain the Carlton Football Club, Judd won the John Nicholls Medal as the club's Best and Fairest three times, and become the fourth player in AFL history to win a Brownlow Medal at more than one club.[3]

Judd was a graduate of the 2000 AIS/AFL Academy and participated in the 2000 AFL Under-18 Championships, although due to his young age at 17, he was too young to be drafted by an AFL club. He played TAC Cup football with the Sandringham Dragons through to 2001.

At the 2001 AFL National Under 18 Championships, Judd was named captain of the Vic Metro team, despite chronic shoulder problems.[8] Although he missed the 2001 AFL Draft Camp, his performances at the state championships made him an obvious standout to recruiters and was tipped to be picked high in the 2001 AFL Draft. Judd was taken by West Coast with its priority draft pick (No. 3 overall) in what was later to be called the "super draft" due to the standout quality of the players to have developed from that draft year.

Judd played only one WAFL match[9] before making his debut for West Coast in Round 2, 2002. He had an impressive debut season, winning the AFLPA Best First Year Player Award. In his second season, he alternated between the midfield and forward line and with several dominant performances he finished runner up in the club's best and fairest. He was appointed as one of the Eagles' four vice-captains prior to the commencement of the 2004 season.

2004 was Judd's breakthrough season in which he combined with captain Ben Cousins, midfielder Daniel Kerr and ruckmanDean Cox in the Eagles' midfield. Judd averaged 22 disposals and kicked 24 goals for the season and became West Coast's first Brownlow medallist, polling 30 votes to finish seven ahead of runner-up Mark Ricciuto. Additionally, he was named to his first All-Australian team as a wingman, and won the Eagles' Club Champion award for the first time. In 2005, he again averaged 22 disposals and was runner-up to Cousins as Club Champion; he kicked the Goal of the Year and won the Norm Smith Medal in West Coast's four-point loss to Sydney in the 2005 AFL Grand Final.

On 1 March 2006, Judd was named captain of the club, succeeding Ben Cousins who stepped down from the role for disciplinary reasons.[10] He led the Eagles to a one-point victory against Sydney in the 2006 AFL Grand Final, winning his only AFL Premiership medallion. Additionally, he won his second club best and fairest award, his second All-Australian selection and the Leigh Matthews Trophy as the AFL Players Association's Most Valuable Player.

Judd's strong form continued into 2007 and he polled Brownlow votes in each of his first eight games for the season. However, as the year progressed, he was hampered by a chronic groin injury which sidelined him for several weeks and restricted his performance in the games he played. He was forced to play off the bench and in the forward line often and was rested for several games in anticipation of playing in the finals series. He had won one premiership and was runner-up with the West Coast Eagles in 2005.

On 16 September 2007, two days after West Coast's semi-final elimination by Collingwood, it was announced that Judd had left West Coast and would be requesting a trade to a club in Victoria.[11] He notified West Coast coach John Worsfold and CEO Trevor Nisbett of his intentions earlier that day.[12][13] As arguably the most talented player in the competition, his departure created much attention and speculation among the Melbourne-based clubs, the media and the football community.

In the weeks following the announcement of his departure, Judd met with four clubs: Essendon, Melbourne, Collingwood and Carlton.[14] On 2 October 2007, Judd announced that his preferred club was Carlton, and Carlton was also considered most likely to secure the a trade with West Coast, because the club held two early draft picks which could be used in negotiations.[15] On 11 October 2007, Judd was officially traded to Carlton along with a third round selection in the 2007 AFL Draft (No. 46 overall) for Carlton's first and second round selections (No. 3 and 20) and Josh Kennedy, who was reluctant to leave Carlton.[16] Judd was subsequently given the No. 5 guernsey vacated by the trade of Kennedy,[17] and he signed a six-year, $6,000,000 contract with the club.[18]

During the off-season, Judd was awarded the captaincy of the club entering into his first season with the Blues. His first game in navy blue was a Friday afternoon practice match on 7 March 2008 against the Western Bulldogs at MC Labour Park, with his presence attracting 12,000 fans,[19] and he began his senior career with the club in the first round. His return match against West Coast at Subiaco Oval in Round 7 was widely anticipated in the media, and Carlton won by 37 points.[20] Judd played 21 of the 22 home-and-away games through the season was named All-Australian captain and ruck rover – his third All-Australian selection, and first as captain – and won the John Nicholls Medal for the best and fairest of the Carlton Football Club. He also represented the Victorian team the following week for the Hall of Fame Tribute Match. Judd again won the John Nicholls Medal and All-Australian selection in 2009.

Judd had a controversial end to his 2009 season. In Carlton's elimination final loss to Brisbane, Judd was cited by the Match Review Panel for misconduct against Michael Rischitelli, after Judd made unnecessary contact near Rischitelli's eyes. The media initially reported the case as eye-gouging, and Judd created a bigger controversy when he stated that his intention was not to eye-gouge, but to push a pressure point behind Rischitelli's ear. Judd later said that his comment was intended as dry humor, but it was misinterpreted as genuine and prompted condemnation from many sources, from sports commentators to martial arts experts. After contesting the charge and appealing the penalty at the AFL Tribunal, Judd was suspended for three weeks. In another deadpan statement after the hearing, he stated "I've since watched a couple of Steven Seagal movies and realised that pressure points are no laughing matter," but he also acknowledged his own "stupidity" in the controversy.[21][22] Then, his leadership was called into question when the team misbehaved during an organised Christmas booze cruise, which saw suspensions to teammates Andrew Walker, Eddie Betts and Ryan Houlihan.[23]

After missing the opening three rounds of the 2010 season due to the "pressure point" incident, Judd earned three Brownlow votes in each of his first five matches for the season, going on to win his second Brownlow Medal with 30 votes, four ahead of 2009 Brownlow Medallist Gary Ablett, Jr.. He became the thirteenth VFL/AFL player to win the Brownlow more than once, the fourth VFL/AFL player to win the Brownlow at two different clubs (West Coast and Carlton), and the first VFL/AFL player to twice poll thirty or more votes in a season.[24] Judd also won his fifth All-Australian selection, being named on the interchange bench, and his third consecutive John Nicholls Medal, becoming the only player other than Nicholls to win the Carlton best and fairest award three times in a row.[25]

In 2011, Judd led Carlton to its best season in a decade, helping the team finish 5th at the end of the season, and to record its first finals victory since 2001. He was awarded the Leigh Matthews Trophy for the second time in his career, as well as the AFLPA's Best Captain Award for the first time.[26] He was named vice-captain and ruck-rover of the All-Australian team, his fourth consecutive selection.[27][28] He had entered the Brownlow Medal count as an unbackable favourite, with TAB Sportsbet electing to pay out early after Round 20, but he ultimately finished fifth.[29] He played his 200th AFL game during the season.

In 2012, Judd played his 100th match for Carlton as captain against Hawthorn in round 14. In round 16 against North Melbourne he was reported for misconduct in that he pulled opposition player Leigh Adams' arm up, causing the shoulder to dislocate, in a move known as a "chicken wing tackle". Judd denied that he intended to hurt Adams, but the tribunal found him guilty and suspended him for four matches.[30][31] He finished third in the John Nicholls Medal for the 2012 season.[32]

Following the 2012 season, Judd took on a smaller role in the team, electing to relinquish the captaincy and step down from the leadership group.[1] After his original six-year contract ended at the end of 2013, he began signing single-year contracts in preparation for the end of his career.[18] Early in 2015, Geelong player, Cameron Guthrie asked Judd to do a guernsey swap which Judd agreed to. This was a sign of respect for Judd from Guthrie, and although the Blues were beaten that night, it showed how sincere and kind Judd is. In Round 10, 2015, he suffered an anterior cruciate ligament injury in his left knee[33] and subsequently announced his retirement days later, bringing an end to his 279 game career.[34]

At his peak, Judd was the best midfielder in the game and is widely regarded as one of the best players of the 2000s decade. The strengths and traits of Judd's playing style were different between his time at West Coast and his time at Carlton, and he has been widely lauded for his proficiency at both. At West Coast, while he was a strong ball-winner, it was as an outside midfielder and ball-user where he distinguished himself. He possessed a combination of explosive speed, acceleration, agility and core strength which few if any players in the league could match; these attributes gave him the ability to receive the ball in traffic, then break free from or weave around taggers and opponents, allowing him to take clearing kicks in open space which were damaging to opposition teams. By the time he had joined Carlton, he had lost much of his acceleration and agility owing to the groin injuries he suffered in 2007. He overcame this by converting his game style to predominantly inside ball-winning role. By virtue of his core strength and balance, he became one of the best in the league at receiving ruck tap-outs, and riding or shaking off tackles in packs and congestion to win clearing handpasses to Carlton's outside midfielders.[35][36][37]

He is the hardest opponent I've ever played on. I remember watching him when he first burst on to the scene, I actually would look at him as someone I wanted to base my game around. His speed, his accuracy with his skills, his contested football. It's just fantastic.

I played with magnificent players. Nicholls, Doull, Jesaulenko, but Judd is by far the best I've ever seen. He is just so consistently good, week after week - the way he's going he will win another Brownlow.

Towards the end of 2003, Judd began writing a column on the West Coast Eagles official website called "Juddy's Jibe". Some of his opinions presented in these columns prompted extensive media commentary, such as his view that footballers should not be role models. Throughout the 2006 season, the column was also published in Melbourne newspaper The Age, in which Judd wrote about issues such as global warming, terrorism, superficiality in the mass media, world peace and James Surowiecki's book The Wisdom of Crowds.

In 2009, Judd was featured in the official advertisement for the AFL, receiving a mark from Aaron Davey on a basketball court and then sprinting in front of a stampede of horses on a horse racing track before handballing to Adam Goodes.